MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 2000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid building block
Residue Name (RNME)KMN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17168
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:14
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17531 None - 18 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)